Table 3. Allele frequencies of polymorphisms in FC27-like msp2 of P. falciparum isolates from mild, severe and cerebral malaria patients in Thailand.
| Region | Polymorphic positiona | Mild | Severe ((S)(S) | Cerebral | Total | M vs Sd | M vs C | S vs C | |
|---|---|---|---|---|---|---|---|---|---|
| Nucleotide | Codon (aa.) | (%) | (%) | (%) | (%) | P-value, OR | P-value,OR | P-value,OR | |
| Block 2 | 23 A/Cb | 8 AAG (K) | 19 (35.2) | 7 (25.0) | 13 (40.6) | 39 (34.2) | 0.347, 0.61 | 0.614, 1.26 | 0.200, 2.05 |
| 24 G/T | · · T (N) | 13 (24.1) | 13 (46.4) | 7 (21.9) | 33 (28.9) | 0.039, 2.73 | 0.816, 0.88 | 0.044, 0.32 | |
| · CT (T) | 22 (40.7) | 8 (28.6) | 12 (37.5) | 42 (36.8) | 0.278, 0.58 | 0.766, 0.87 | 0.464, 1.50 | ||
| 27 T/G | 9 AGT (S) | 45 (83.3) | 18 (64.3) | 26 (81.3) | 89 (78.1) | 0.053, 2.78 | 0.806, 1.15 | 0.138, 0.42 | |
| · ·G (R) | 9 (16.7) | 10 (35.7) | 6 (18.8) | 25 (21.9) | |||||
| 32 G/A | 11 GGT (G) | 51 (94.4) | 25 (89.3) | 31 (96.9) | 107 (93.9) | NA. | NA. | NA. | |
| · A · (D) | 3 (5.6) | 3 (10.7) | 1 (3.1) | 7 (6.1) | |||||
| 37 A/G | 13 AAT (N) | 50 (92.6) | 25 (89.3) | 31 (96.9) | 106 (93.0) | NA. | NA. | NA. | |
| 39 T/A | · · A (K) | 3 (5.6) | 3 (10.7) | 1 (3.1) | 7 (6.1) | NA. | NA. | NA. | |
| G· · (D) | 1 (1.9) | 0 (0) | 0 (0) | 1 (0.9) | NA. | NA. | NA. | ||
| 48 A/T | 16 AAA (K) | 33 (61.1) | 18 (64.3) | 21 (65.6) | 72 (63.2) | 0.779, 0.87 | 0.676, 0.82 | 0.914, 0.94 | |
| · · T (N) | 21 (38.9) | 10 (35.7) | 11 (34.4) | 42 (36.8) | |||||
| 49_57indel | 17_19 del | 53 (98.1) | 26 (92.9) | 32 (100.0) | 111 (97.4) | NA. | NA. | NA. | |
| 17_19 ins GCT CCA AAA (APK) | 0 (0) | 2 (7.1) | 0 (0) | 2 (1.8) | NA. | NA. | NA. | ||
| 17_19 ins GCT CCA AAT (APN) | 1 (1.9) | 0 (0) | 0 (0) | 1 (0.9) | NA. | NA. | NA. | ||
|
Block3c |
(R1)n(R2)n | (R1)(R2)(R2) | 1 (1.9) | 2 (7.1) | 0 (0) | 3 (2.6) | NA. | NA. | NA. |
| (R1)(R2)(R2)(R2) | 39 (72.2) | 22 (78.6) | 21 (65.6) | 82 (71.9) | 0.532, 1.41 | 0.520, 0.73 | 0.267, 0.52 | ||
| (R1)(R2)(R2)(R2)(R2) | 7 (13.0) | 3 (10.7) | 9 (28.1) | 19 (16.7) | 0.768, 0.81 | 0.081, 2.63 | 0.093, 3.26 | ||
| (R1)(R2)(R2)(R2)(R2)(R2) | 5 (9.3) | 1 (3.6) | 1 (3.1) | 7 (6.1) | NA. | NA. | NA. | ||
| (R1)(R1)(R1)(R2) | 2 (3.7) | 0 (0) | 1 (3.1) | 3 (2.6) | NA. | NA. | NA. | ||
| R1xR2 | A 12 | 1 (1.9) | 0 (0) | 0 (0) | 1 (0.9) | NA. | NA. | NA. | |
| Block 3c | A 122 | 20 (37.0) | 15 (53.6) | 11 (34.4) | 46 (40.3) | 0.151, 1.96 | 0.804, 0.89 | 0.134, 0.45 | |
| A 1222 | 6 (11.1) | 0 (0) | 7 (21.9) | 13 (11.4) | 0.066 | 0.178, 2.24 | 0.009 | ||
| A 132 | 2 (3.7) | 1 (3.6) | 0 (0) | 3 (2.6) | NA. | NA. | NA. | ||
| A 1333 | 0 (0) | 2 (7.1) | 0 (0) | 2 (1.8) | NA. | NA. | NA. | ||
| A 222 | 3 (5.6) | 0 (0) | 0 (0) | 3 (2.6) | NA. | NA. | NA. | ||
| A 333 | 14 (25.9) | 6 (21.4) | 10 (31.3) | 30 (26.3) | 0.653, 0.78 | 0.595, 1.30 | 0.391, 1.67 | ||
| A 3333 | 0 (0) | 0 (0) | 2 (6.3) | 2 (1.8) | NA. | NA. | NA. | ||
| A 33333 | 5 (9.3) | 1 (3.6) | 1 (3.1) | 7 (6.1) | NA. | NA. | NA. | ||
| B 22 | 0 (0) | 2 (7.1) | 0 (0) | 2 (1.8) | NA. | NA. | NA. | ||
| B 2222 | 0 (0) | 1 (3.6) | 0 (0) | 1 (0.9) | NA. | NA. | NA. | ||
| C 2111 | 1 (1.9) | 0 (0) | 0 (0) | 1 (0.9) | NA. | NA. | NA. | ||
| ADD 2 | 2 (3.7) | 0 (0) | 1 (3.1) | 3 (2.6) | NA. | NA. | NA. | ||
| Block 4 | 58 G/A | 20 GAA (E) | 43 (79.6) | 24 (85.7) | 30 (93.8) | 97 (85.1) | 0.499, 0.65 | 0.077, 0.26 | 0.301, 0.4 |
| A · · (K) | 11 (20.4) | 4 (14.3) | 2 (6.3) | 17 (14.9) | |||||
| 64 C/A | 22 CAA (Q) | 44 (81.5) | 24 (85.7) | 30 (93.8) | 98 (86.0) | 0.629, 0.73 | 0.113, 0.29 | 0.301, 0.4 | |
| A · · (K) | 10 (18.5) | 4 (14.3) | 2 (6.3) | 16 (14.0) | |||||
a Position relative to the first nucleotide / aa. of each block (Fig 2).
b In case of SNPs, alleles found in the msp2 sequence of K1 (FC27-liked) (M59766.1) / another found in our data set was shown and amino acid (aa.) changes were indicated.
c Variation in number of repeat 1 and 2 [(R1)n(R2)n] generated 5 distinct alleles in block 3, while 13 alleles were detected when sequence variation in repeat units were considered [R1xR2].
d Allele frequencies were compared between mild (M) and severe (S), mild and cerebral (C), as well as severe and cerebral. For bi-allelic polymorphisms, the odds ratio (OR) of a minor-frequency allele for risk to severe and cerebral malaria by comparing to a major allele was analyzed. For polymorphisms with more than 2 alleles, the presence or absence of individual alleles were compared. OR and P-values are shown, with significant values in bold. NA. (not applicable) indicates bi-allelic polymorphisms with minor allele frequency <10% and individual alleles having frequencies <10% or >90%, in which their associations with malaria severity were not analyzed. OR was undefined in cases of zero cell count.